Variant report

Variant	rs12971376
Chromosome Location	chr19:42439907-42439908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42366038..42367665-chr19:42439832..42441415,2	K562	blood:
2	chr19:42389824..42391780-chr19:42439808..42442241,2	K562	blood:
3	chr19:42389371..42391920-chr19:42438453..42441265,2	MCF-7	breast:
4	chr19:42390344..42392993-chr19:42439270..42441134,2	MCF-7	breast:
5	chr19:42434761..42437338-chr19:42437416..42440186,3	MCF-7	breast:
6	chr19:42375846..42378575-chr19:42437686..42441355,5	MCF-7	breast:
7	chr19:42366028..42368892-chr19:42439399..42440962,2	MCF-7	breast:
8	chr19:42363084..42365326-chr19:42439152..42440744,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10409822	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10411814	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414709	0.84[ASN][1000 genomes]
rs10416501	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10419731	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420264	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10424013	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11083642	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11665965	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11667048	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668332	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669448	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11878287	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12975677	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1864207	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1965727	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2081999	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745223	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826707	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61007366	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246830	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247727	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7253563	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs735571	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109192	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919390	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9304600	0.83[EUR][1000 genomes]
rs9676662	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9749440	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12971376	RABAC1	cis	multi-tissue	Pritchard
rs12971376	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42433200-42441400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:42433600-42444000	Weak transcription	Right Atrium	heart
3	chr19:42437800-42440000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr19:42437800-42440600	Enhancers	Primary T cells from cord blood	blood
5	chr19:42437800-42441200	Enhancers	Primary B cells from peripheral blood	blood
6	chr19:42437800-42442600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr19:42437800-42442600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr19:42438200-42441800	Enhancers	K562	blood
9	chr19:42438400-42440800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr19:42438400-42440800	Enhancers	Esophagus	oesophagus
11	chr19:42438400-42441400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:42438600-42441000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:42438800-42441400	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr19:42439000-42440000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:42439000-42440200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:42439200-42440000	Enhancers	Osteobl	bone
17	chr19:42439200-42440200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
18	chr19:42439200-42440200	Weak transcription	A549	lung
19	chr19:42439200-42440400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:42439200-42441200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:42439200-42441600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr19:42439400-42440000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:42439400-42440200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:42439400-42440200	Enhancers	HSMM	muscle
25	chr19:42439400-42440400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:42439400-42440400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
27	chr19:42439400-42440800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:42439400-42440800	Bivalent Enhancer	GM12878-XiMat	blood
29	chr19:42439600-42440200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
30	chr19:42439600-42440600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:42439600-42440800	Bivalent Enhancer	Fetal Stomach	stomach
32	chr19:42439600-42441000	Bivalent Enhancer	NHLF	lung
33	chr19:42439600-42441200	Bivalent Enhancer	NH-A	brain
34	chr19:42439600-42444000	Weak transcription	Spleen	Spleen
35	chr19:42439800-42440000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:42439800-42440200	Bivalent Enhancer	NHEK	skin
37	chr19:42439800-42441000	Enhancers	HMEC	breast
38	chr19:42439800-42442000	Weak transcription	Primary B cells from cord blood	blood
39	chr19:42439800-42443600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr19:42439800-42443800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:42439800-42444600	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links